Reference sequence (1): ORF1AB_China_Dec2019a Identities normalised by aligned length. Colored by: identity |
cov pid 1 [ . . . . : . . . . 1 . . 120 1 ORF1AB_China_Dec2019a 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPH------------------ELV-- 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS--ARTAPHG-------------HVMVELV-- 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-EARTAPHG-------------HVMVELV-- 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 14 ORF1AB_China_11Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 30 ORF1AB_China_08Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 36 ORF1AB_China_02Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 37 ORF1AB_USA_19Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV-- 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLCG--------SGNLVEKL----SPWFMDGENAYEVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQLAY 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLCG--------SGNLVEKL----SPWFMDGENAYEVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQLAY 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLCG--------SGNLVEKL----SPWFMDGENAYEVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQLAY 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLCG--------SGNLVEKL----SPWFMDGENAYEVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQLAY consensus/100% ...............hcuhlsu.pcpsHVpLolPlht.........Gs.VEcl....p.ahhDGpsuh..VcthlL.p....YV.I+hu..sRphPt..................p.l.. consensus/90% ...............MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS.cARTAPHs..............hMVELV.. consensus/80% ...............MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS.DARTAPHG.............HVMVELV.. consensus/70% ...............MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS.DARTAPHG.............HVMVELV.. cov pid 121 . . : . . . . 2 . . . . 240 1 ORF1AB_China_Dec2019a 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 2 ORF1a_Finland_29Jan2020 61.9% 99.6% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADL---DLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 14 ORF1AB_China_11Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 30 ORF1AB_China_08Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 36 ORF1AB_China_02Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 37 ORF1AB_USA_19Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% SSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGRGGYHYTPFHYE---------RDNTSCPEWMDDFEADPKGKYAQNLLKKLIGGDV-TPVDQYMCGVDGKPISAYAFLMA 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% SSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGRGGYHYTPFHYE---------RDNTSCPEWMDDFEADPKGKYAQNLLKKLIGGDV-TPVDQYMCGVDGKPISAYAFLMA 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% SSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGRGGYHYTPFHYE---------RDNTSCPEWMDDFEADPKGKYAQNLLKKLIGGDV-TPVDQYMCGVDGKPISAYAFLMA 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% SSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGRGGYHYTPFHYE---------RDNTSCPEWMDDFEADPKGKYAQNLLKKLIGGDV-TPVDQYMCGVDGKPISAYAFLMA consensus/100% .uphpG..lthshpGcslGhhhPashElssuhpplLLRK.GptGhthpsath-.........hssssh.-a.-sapsc.puthsppLh+cL.GGsh.p.VDp.hCGsDGhPlpsht.LhA consensus/90% .AELEG..IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADL...DLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA consensus/80% .AELEG..IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA consensus/70% .AELEG..IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA cov pid 241 : . . . . 3 . . . . : . 360 1 ORF1AB_China_Dec2019a 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 2 ORF1a_Finland_29Jan2020 61.9% 99.6% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 14 ORF1AB_China_11Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 30 ORF1AB_China_08Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 36 ORF1AB_China_02Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 37 ORF1AB_USA_19Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% KDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPP-HYFTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAFIE 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% KDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPP-HYFTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAFIE 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% KDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPP-HYFTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAFIE 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% KDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPP-HYFTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAFIE consensus/100% +sGhsphs.s.tplshhssccGhhsh+pp.aclsWasERp-hsY.hQo.FpIp.shphDshpspsP.ahFsLsshIhTlpPRschptlssh.h+.+....hYshtS.ppss.hhhSshhc consensus/90% RAGKASCTLS.EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS...VYPVASPNECNQMCLSTLMK consensus/80% RAGKASCTLS.EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS...VYPVASPNECNQMCLSTLMK consensus/70% RAGKASCTLS.EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS...VYPVASPNECNQMCLSTLMK cov pid 361 . . . 4 . . . . : . . . 480 1 ORF1AB_China_Dec2019a 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 2 ORF1a_Finland_29Jan2020 61.9% 99.6% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 14 ORF1AB_China_11Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRANANIGCNHT 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 30 ORF1AB_China_08Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 36 ORF1AB_China_02Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 37 ORF1AB_USA_19Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% CGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSE-RCNVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRIGD 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% CGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSE-RCNVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRIGD 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% CGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSE-RCNVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRIGD 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% CGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSE-RCNVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRIGD consensus/100% CspCGpsSW.TGshlpuhsphCGsp.hsp-.tsposGhl..NAllphhCPhs+sspsus..cHSl...spYhsE.thpsIhcptuhTlhFGGssauYhGCcptshYaVPRApuslup.ts consensus/90% CDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCPACHNSEVGP..EHSL...AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRAsANIGCNHT consensus/80% CDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCPACHNSEVGP..EHSL...AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT consensus/70% CDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCPACHNSEVGP..EHSL...AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT cov pid 481 . 5 . . . . : . . . . 6 600 1 ORF1AB_China_Dec2019a 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 2 ORF1a_Finland_29Jan2020 61.9% 99.6% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 14 ORF1AB_China_11Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 30 ORF1AB_China_08Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 36 ORF1AB_China_02Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 37 ORF1AB_USA_19Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% SIFT-GCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKVAT 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% SIFT-GCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKVAT 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% SIFT-GCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKVAT 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% SIFT-GCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKVAT consensus/100% ulhs.GspG..s.....h..hLpppphslNhVG-FhlN-.lhhILuuhossssthhphlKGlshcth+phltsh.shtVTtG.hhcsAhNlGtpt....hlos.Yshhothucs...Vto consensus/90% GVVGEGSEGLND....NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS...ILSPLYAFASEAARV...VRS consensus/80% GVVGEGSEGLND....NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS...ILSPLYAFASEAARV...VRS consensus/70% GVVGEGSEGLND....NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS...ILSPLYAFASEAARV...VRS cov pid 601 . . . . : . . . . 7 . . 720 1 ORF1AB_China_Dec2019a 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 2 ORF1a_Finland_29Jan2020 61.9% 99.6% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 14 ORF1AB_China_11Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 30 ORF1AB_China_08Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 36 ORF1AB_China_02Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 37 ORF1AB_USA_19Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% IPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCVDLSVA--ST-----YFLVRLLQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYVY- 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% IPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCVDLSVA--ST-----YFLVRLLQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYVY- 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% IPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCVDLSVA--ST-----YFLVRLLQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYVY- 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% IPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCVDLSVA--ST-----YFLVRLLQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYVY- consensus/100% I..+shpospsolph......hphhshsh.sGlSpaS.hLhDsh.hoss..os.....halsthl.phTupaho...........plhsTsaEthcsshsaL.-hht.hh.FLRsua.h. consensus/90% IFSRTLETAQNSVRV......LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT...........NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV consensus/80% IFSRTLETAQNSVRV......LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT...........NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV consensus/70% IFSRTLETAQNSVRV......LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT...........NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV cov pid 721 . . : . . . . 8 . . . . 840 1 ORF1AB_China_Dec2019a 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 2 ORF1a_Finland_29Jan2020 61.9% 99.6% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 14 ORF1AB_China_11Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 30 ORF1AB_China_08Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 36 ORF1AB_China_02Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 37 ORF1AB_USA_19Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ---TSQGFVVVNGKVSTLV-------KQVLDLLNKGMQLLHTKVSWAGFNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVT-------- 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ---TSQGFVVVNGKVSTLV-------KQVLDLLNKGMQLLHTKVSWAGSNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVT-------- 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% ---TSQGFVVVNGKVSTLV-------KQVLDLLNKGMQLLHTKVSWAGSNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVT-------- 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% ---TSQGFVVVNGKVSTLV-------KQVLDLLNKGMQLLHTKVSWAGFNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVT-------- consensus/100% ...oopuh.lVsGplsThs.......pphhcLlNKhhtLhtspl.huG.plpAl...Gcp.lhaspGhYh.CVp..................S+cphGLL.Phcssppl.hh........ consensus/90% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN.LGETFVTHSKGLYRKCVK..................SREETGLLMPLKAPKEIIFLEGETLPTE consensus/80% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN.LGETFVTHSKGLYRKCVK..................SREETGLLMPLKAPKEIIFLEGETLPTE consensus/70% KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN.LGETFVTHSKGLYRKCVK..................SREETGLLMPLKAPKEIIFLEGETLPTE cov pid 841 : . . . . 9 . . . . : . 960 1 ORF1AB_China_Dec2019a 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 2 ORF1a_Finland_29Jan2020 61.9% 99.6% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGSAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 14 ORF1AB_China_11Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 30 ORF1AB_China_08Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 36 ORF1AB_China_02Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 37 ORF1AB_USA_19Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% VSSNMVETVVGQL---EQTN-MHSPDVIVGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSL 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% VSSNMVETVVGQL---EQTN-MHSPDVIVGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSL 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% VSSNMVETVVGQL---EQTN-MHSPDVIVGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% VSSNMVETVVGQL---EQTN-MHSPDVIVGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSL consensus/100% V.op.V.hhsGpL...EQss..ts.sslVGs.VhIsthhhlc.K-p-ta..hshssNhhsssshFpLKGuAPs.KVsFGsDpVhEVtuh+SVslpaplcthlDplLspp.hpsasV-huh consensus/90% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY..CALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK.CSAYTVELGT consensus/80% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY..CALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK.CSAYTVELGT consensus/70% VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY..CALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK.CSAYTVELGT cov pid 961 . . . 0 . . . . : . . . 1080 1 ORF1AB_China_Dec2019a 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 2 ORF1a_Finland_29Jan2020 61.9% 99.6% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQE-EEQEE--D 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSIATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQLEEEQEE--D 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 14 ORF1AB_China_11Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 30 ORF1AB_China_08Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 36 ORF1AB_China_02Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 37 ORF1AB_USA_19Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% SIEEFADVVKEQVSDLLVKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEISDDEWAAAVDEAFPLDEAEDVTE 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% SIEEFADVVKEQVSDLLVKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEVSDDEWAAAVDEAFPLDEAEDVTE 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% SIEEFADVVKEQVSDLLVKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEVSDDEWAAAVDEAFPLDEAEDVTE 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% SIEEFADVVKEQVSDLLVKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEISDDEWAAAVDEAFPLDEAEDVTE consensus/100% plpEFAsVVt-tV.chL..l.chhs..shDLD-a..AshYhFstpG-hphuSpMhhShaPs-pDEEpu-sEtp-hE.upp.ph...uTEps..u...ps.EauAsssth...-EtE-..- consensus/90% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWShATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY...GTEDDYQG...KPLEFGATSAALQP.EEQEE..D consensus/80% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY...GTEDDYQG...KPLEFGATSAALQPEEEQEE..D consensus/70% EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY...GTEDDYQG...KPLEFGATSAALQPEEEQEE..D cov pid 1081 . 1 . . . . : . . . . 2 1200 1 ORF1AB_China_Dec2019a 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 2 ORF1a_Finland_29Jan2020 61.9% 99.6% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 14 ORF1AB_China_11Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 30 ORF1AB_China_08Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 36 ORF1AB_China_02Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 37 ORF1AB_USA_19Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% SVQEEAQPVEVPVEDIAQVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRIKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLV 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% SVQEEAQPVEVPVEDIAQVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRKKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLV 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% SVQEEAQPVEVPVEDIAQVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRKKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% SVQEEAQPVEVPVEDIAQVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRIKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLV consensus/100% .lp--uQ..pVs.pDh.....u.p.ppTsslpshVEV.PQl.h.............ElsPVhp..................phpVsshSsa..hhlT-sVhIh.uDhlp.AKpht.oVlV consensus/90% WLDDDSQQ.TVGQQDG.....S.EDNQTTTIQTIVEVQPQLEM.............ELTPVVQ..................TIEVNSFSGY..LKLTDNVYIKNADIVEEAKKVKPTVVV consensus/80% WLDDDSQQ.TVGQQDG.....S.EDNQTTTIQTIVEVQPQLEM.............ELTPVVQ..................TIEVNSFSGY..LKLTDNVYIKNADIVEEAKKVKPTVVV consensus/70% WLDDDSQQ.TVGQQDG.....S.EDNQTTTIQTIVEVQPQLEM.............ELTPVVQ..................TIEVNSFSGY..LKLTDNVYIKNADIVEEAKKVKPTVVV cov pid 1201 . . . . : . . . . 3 . . 1320 1 ORF1AB_China_Dec2019a 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 2 ORF1a_Finland_29Jan2020 61.9% 99.6% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQFESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 14 ORF1AB_China_11Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 30 ORF1AB_China_08Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 36 ORF1AB_China_02Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 37 ORF1AB_USA_19Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% NAANTHLKHGGGIAGAINAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVN 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% NAANTHLKHGGGIAGAINAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVN 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% NAANTHLKHGGGIAGAINAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVN 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% NAANTHLKHGGGIAGAINAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVN consensus/100% NAANsaLKHGGGlAGAlNtAopsAhQhESD-YIhspGPLpVGsSslLpGHsLAKphLHVVGPsspttpDlpLLppsYcshNta.lllsPLlSAGIFGscPhhShchhlcps+TpVhlsV. consensus/90% NAANVYLKHGGGVAGALNKATNNAMQhESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF consensus/80% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF consensus/70% NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF cov pid 1321 . . : . . . . 4 . . . . 1440 1 ORF1AB_China_Dec2019a 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 2 ORF1a_Finland_29Jan2020 61.9% 99.6% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 14 ORF1AB_China_11Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 30 ORF1AB_China_08Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 36 ORF1AB_China_02Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 37 ORF1AB_USA_19Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% SQDVYKSLTI---------------VDIPQSLT------------------------------------------FSYDGLRGA------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% SQDVYKSLTI---------------VDIPQSLT------------------------------------------FSYDGLRGA------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% SQDVYKSLTI---------------VDIPQSLT------------------------------------------FSYDGLRGA------------------------------------ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% SQDVYKSLTI---------------VDIPQSLT------------------------------------------FSYDGLRGA------------------------------------ consensus/100% spslYcpLs................s-IPpp.s..........................................h.Y.slpGs.................................... consensus/90% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA consensus/80% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA consensus/70% DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA cov pid 1441 : . . . . 5 . . . . : . 1560 1 ORF1AB_China_Dec2019a 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 2 ORF1a_Finland_29Jan2020 61.9% 99.6% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 14 ORF1AB_China_11Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 30 ORF1AB_China_08Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 36 ORF1AB_China_02Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 37 ORF1AB_USA_19Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------IRKAKD---------Y---GFT--------------------------------------------------VFVCTDNSANTKV--LRNKGVDYTKKFLTV 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------IRKAKD---------Y---GFT--------------------------------------------------VFVCTDNSANTKV--LRNKGVDYTKKFLTV 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% ------------------IRKAKD---------Y---GFT--------------------------------------------------VFVCTDNSANTKV--LRNKGVDYTKKFLTV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% ------------------IRKAKD---------Y---GFT--------------------------------------------------VFVCTDNSANTKV--LRNKGVDYTKKFLTV consensus/100% ..................lRKs.s.............GaT..................................................h.VCs-spA.sps..h+.KGlchpc.hlss consensus/90% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE.GVVD consensus/80% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE.GVVD consensus/70% VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE.GVVD cov pid 1561 . . . 6 . . . . : . . . 1680 1 ORF1AB_China_Dec2019a 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 2 ORF1a_Finland_29Jan2020 61.9% 99.6% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 14 ORF1AB_China_11Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 30 ORF1AB_China_08Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 36 ORF1AB_China_02Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 37 ORF1AB_USA_19Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% DGVQYYCYTSKDTLDDILQQAN-KSVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAIL--MSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLNKLLHWSDQ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% DGVQYYCYTSKDTLDDILQQAN-KSVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAIL--MSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLNKLLHWSDQ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% DGVQYYCYTSKDTLDDILQQAN-KSVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAIL--MSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLNKLLHWSDQ 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% DGVQYYCYTSKDTLDDILQQAN-KSVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAIL--MSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLNKLLHWSDQ consensus/100% .GspaYhYTSKsTlssllpphN.hs.slloMPLGYVoHGLsL.pAuphhRplpVPhss.lus.-t.shh..h.pssphsPpEcFIcplphsGuYpsWphsttph.lt.....chL+huDp consensus/90% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI....EFLKRGDK consensus/80% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI....EFLKRGDK consensus/70% YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI....EFLKRGDK cov pid 1681 . 7 . . . . : . . . . 8 1800 1 ORF1AB_China_Dec2019a 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 2 ORF1a_Finland_29Jan2020 61.9% 99.6% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 14 ORF1AB_China_11Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 30 ORF1AB_China_08Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 36 ORF1AB_China_02Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 37 ORF1AB_USA_19Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% TICYKDSVFYVVKNSTAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHRFY 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% TICYKDSVFYVVKNSTAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHRFY 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% TICYKDSVFYVVKNSTAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHRFY 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% TICYKDSVFYVVKNSTAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHRFY consensus/100% olhYpssshhhhhsupshsF-sLps...hLs..hpp.hTIcVhsTVDslNh+T.Vls.p.TYtpQhGssahsGADlochhPcppppG+ohYlhsN.ss.cs.thhEhYtssDPoFLtRah consensus/90% SVYYTSNPTTFHLDGEVITFDNLKT...LLS..LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV.EAFEYYHTTDPSFLGRYM consensus/80% SVYYTSNPTTFHLDGEVITFDNLKT...LLS..LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV.EAFEYYHTTDPSFLGRYM consensus/70% SVYYTSNPTTFHLDGEVITFDNLKT...LLS..LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV.EAFEYYHTTDPSFLGRYM cov pid 1801 . . . . : . . . . 9 . . 1920 1 ORF1AB_China_Dec2019a 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 2 ORF1a_Finland_29Jan2020 61.9% 99.6% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHXNLD-SCKRVLNVVCKTCGQQQTTLKGV 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 14 ORF1AB_China_11Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 30 ORF1AB_China_08Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 36 ORF1AB_China_02Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 37 ORF1AB_USA_19Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% SLKAAVHKWKMVVCDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGL 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% SLKAAVHKWKMVVCDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGSPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGL 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% SLKAAVHKWKMVVCDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGSPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% SLKAAVHKWKMVVCDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGL consensus/100% Shhsts+KWKhs.sstlpSlKhuDNNCYLssslhTLp.l.-lKFs.PALQcAah+t+uG-ussFhALIhAYsNpThGt.sDspchhphlht+.pLs.Ss+hVhp.hCpsCG.ppssLpGl consensus/90% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD.SCKRVLNVVCKTCGQQQTTLKGV consensus/80% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD.SCKRVLNVVCKTCGQQQTTLKGV consensus/70% SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD.SCKRVLNVVCKTCGQQQTTLKGV cov pid 1921 . . : . . . . 0 . . . . 2040 1 ORF1AB_China_Dec2019a 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 2 ORF1a_Finland_29Jan2020 61.9% 99.6% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 14 ORF1AB_China_11Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 30 ORF1AB_China_08Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 36 ORF1AB_China_02Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 37 ORF1AB_USA_19Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% KACCYVGVQTVEDLRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVV 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% KACCYVGVQTVEDLRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVV 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% KACCYVGVQTVEDLRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% KACCYVGVQTVEDLRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVV consensus/100% cAshYhGs.ohEph+tthphsCpCGtptp+.lVpppoPalhhSusPsph.lppuTh...sshs.apG.phtsGHYhHhp.Kts.lhphDuuhloKoS-aKs.lTDVha.tppYooshpsV consensus/90% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF...TCASEYTG.NYQCGHYKHITSKET.LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV consensus/80% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF...TCASEYTG.NYQCGHYKHITSKET.LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV consensus/70% EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF...TCASEYTG.NYQCGHYKHITSKET.LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV cov pid 2041 : . . . . 1 . . . . : . 2160 1 ORF1AB_China_Dec2019a 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 2 ORF1a_Finland_29Jan2020 61.9% 99.6% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 14 ORF1AB_China_11Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 30 ORF1AB_China_08Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 36 ORF1AB_China_02Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 37 ORF1AB_USA_19Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% RYSLDGNFRTEVDPDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILW 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% RYSLDGNFRTEVDPDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILW 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% RYSLDGNFRTEVDPDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILW 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% RYSLDGNFRTEVDPDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILW consensus/100% pYpLDGshpTElDPcLssaYhKDspYFTppP.s.hsPsp.hssusasN.phVsssh.....thu.shNpLhGa..pKPso+chphoFhPc.sGDVlhh-acpYsP.aKpGAhhhtKPIlW consensus/90% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID.LVPNQPYPNASFDNFKFVCDNI.....KFADDLNQLTGY..KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW consensus/80% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID.LVPNQPYPNASFDNFKFVCDNI.....KFADDLNQLTGY..KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW consensus/70% TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID.LVPNQPYPNASFDNFKFVCDNI.....KFADDLNQLTGY..KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW cov pid 2161 . . . 2 . . . . : . . . 2280 1 ORF1AB_China_Dec2019a 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 2 ORF1a_Finland_29Jan2020 61.9% 99.6% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 14 ORF1AB_China_11Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 30 ORF1AB_China_08Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 36 ORF1AB_China_02Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 37 ORF1AB_USA_19Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% VNKASYDTNLNKFNRASLRQIFDVAPIELENKFTPLSVESTPV---------EP---PTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVL 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% VNKASYDTNLNKFNRASLRQIFDVAPIELENKFTPLSVESTPV---------EP---PTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVL 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% VNKASYDTNLNKFNRASLRQIFDVAPIELENKFTPLSVESTPV---------EP---PTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% VNKASYDTNLNKFNRASLRQIFDVAPIELENKFTPLSVESTPV---------EP---PTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVL consensus/100% hspsuhspsh.K.NphslRplasstPlEhpNpFssLpsEss.s.........cP....sV-ssslQp..sllcCpshsp.hVtD.l.hhssssuh.lsE.lu+pDLhshYVDsp..s.lh consensus/90% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK..DVLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVDNSSLT.IK consensus/80% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK..DVLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVDNSSLT.IK consensus/70% HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK..DVLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVDNSSLT.IK cov pid 2281 . 3 . . . . : . . . . 4 2400 1 ORF1AB_China_Dec2019a 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 2 ORF1a_Finland_29Jan2020 61.9% 99.6% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVC-------FTLLLQLCTFTRST--NSRIKASMPTT---I 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVC-------FTLLLQLCTFTRST--NSRIKASMPTT---I 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRIT--NSRIKASMPTT---I 14 ORF1AB_China_11Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 30 ORF1AB_China_08Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 36 ORF1AB_China_02Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 37 ORF1AB_USA_19Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% KDNVLSSMLRLHTVESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTAVGSCIKSVVRHLGVTKGILTGC-----FSFVKMLFMLPL--AYFSDSKLGTTEVKVSALKTAGVV 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% KDNVLSSMLRLHTVESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTAVGSCIKSVVRHLGVTKGILTGC-----FSFVKMLFMLPL--AYFSDSKLGTTEVKVSALKTAGVV 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% KDNVLSSMLRLHTVESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTAVGSCIKSVVRHLGVTKGILTGC-----FSFVKMLFMLPL--AYFSDSKLGTTEVKVSALKTAGVV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% KDNVLSSMLRLHTVESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTAVGSCIKSVVRHLGVTKGILTGC-----FSFVKMLFMLPL--AYFSDSKLGTTEVKVSALKTAGVV consensus/100% KsN.LSphLtL+TltotslssVs...Slshcs.....hu.YhK.Fhs+s.................lusTpsIlTtC............FhL.L..shFoc.p..soclKsSh.pT...l consensus/90% KPNELSRVLGLKTLATHGLAAVN...SVPWDT.....IANYAKPFLNKV.................VSTTTNIVTRCLNRVChsah.hhFTLLLQLCTFTRST..NSRIKASMPTT...I consensus/80% KPNELSRVLGLKTLATHGLAAVN...SVPWDT.....IANYAKPFLNKV.................VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST..NSRIKASMPTT...I consensus/70% KPNELSRVLGLKTLATHGLAAVN...SVPWDT.....IANYAKPFLNKV.................VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST..NSRIKASMPTT...I cov pid 2401 . . . . : . . . . 5 . . 2520 1 ORF1AB_China_Dec2019a 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 2 ORF1a_Finland_29Jan2020 61.9% 99.6% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 14 ORF1AB_China_11Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 30 ORF1AB_China_08Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 36 ORF1AB_China_02Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% TGNVVKQCCTAAVDLSMDKLRRVDWKSTLRLLLMLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAYRANS-FDVPTFCANRSAMCNWCLISQDSI 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% TGNVVKQCCTAAVDLSMDKLRRVDWKSTLRLLLMLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAYRANS-FDVPTFCANRSAMCNWCLISQDSI 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% TGNVVKQCCTAAVDLSMDKLRRVDWKSTLRLLLMLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAYRANS-FDVPTFCANRSAMCNWCLISQDSI 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% TGNVVKQCCTAAVDLSMDKLRRVDWKSTLRLLLMLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAYRANS-FDVPTFCANRSAMCNWCLISQDSI consensus/100% stNsVKpssphsl-hShshL+pssapphlplllhhh....LLSs.........sLu.slhaps.....thht.lhu.LGhsShCsGhtpuYhsso.hslsTaCs.tSh.CshCL.u.DSl consensus/90% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL....LLSV.........CLG.SLIYST.....AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT.GSIPCSVCLSGLDSL consensus/80% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL....LLSV.........CLG.SLIYST.....AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT.GSIPCSVCLSGLDSL consensus/70% AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL....LLSV.........CLG.SLIYST.....AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT.GSIPCSVCLSGLDSL cov pid 2521 . . : . . . . 6 . . . . 2640 1 ORF1AB_China_Dec2019a 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 2 ORF1a_Finland_29Jan2020 61.9% 99.6% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLI-----MAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLI-----MAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 14 ORF1AB_China_11Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 30 ORF1AB_China_08Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 36 ORF1AB_China_02Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 37 ORF1AB_USA_19Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% THYPALKMVQTHLSHYVLNIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWL----FTHIPMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLC 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% THYPALKMVQTHLSHYVLNIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWL----FTHIPMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLC 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% THYPALKMVQTHLSHYVLNIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWL----FTHIPMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLC 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% THYPALKMVQTHLSHYVLNIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWL----FTHIPMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLC consensus/100% spYPuLchlQhplSpahhslshhhhshEhhLAYhLaTphF.hLhLAuhhphFFu.hula..ahS....sS.hhWL......hhPhuuhVRMY.hhAshahlhK.Y.HVlsGCpsosChhC consensus/90% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH..FIS....NSWLMWLI...hpMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC consensus/80% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH..FIS....NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC consensus/70% DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH..FIS....NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC cov pid 2641 : . . . . 7 . . . . : . 2760 1 ORF1AB_China_Dec2019a 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 2 ORF1a_Finland_29Jan2020 61.9% 99.6% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 14 ORF1AB_China_11Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 30 ORF1AB_China_08Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 36 ORF1AB_China_02Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 37 ORF1AB_USA_19Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN-- 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% YKRNRLTRVEASTVVCGGKRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEV 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% YKRNRLTRVEASTVVCGGKRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEV 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% YKRNRLTRVEASTVVCGGKRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% YKRNRLTRVEASTVVCGGKRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEV consensus/100% YKRNRhTRVEsoTlVsGs+RoFYlhANGGhuFC+hHNWNCVsCDThssGsTFIs-EVApDLohth+RPINsTDpSpYhVDSVTVKpsslph.ac+sGQ.hYERasLstFsNLDpL+hp.. consensus/90% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN.. consensus/80% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN.. consensus/70% YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN.. cov pid 2761 . . . 8 . . . . : . . . 2880 1 ORF1AB_China_Dec2019a 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 2 ORF1a_Finland_29Jan2020 61.9% 99.6% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 14 ORF1AB_China_11Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% --NTKVSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 30 ORF1AB_China_08Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 36 ORF1AB_China_02Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 37 ORF1AB_USA_19Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% CKTTTGIPEYNFIIYDSSDRGQESLARSACVYYSQVLCKSILLVDSSLVTSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVE 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% CKTTTGIPEYNFIIYDSSDRGQESLARSACVYYSQVLCKSILLVDSSLITSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVE 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% CKTTTGIPEYNFIIYDSSDRGQESLARSACVYYSQVLCKSILLVDSSLITSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVE 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% CKTTTGIPEYNFIIYDSSDRGQESLARSACVYYSQVLCKSILLVDSSLVTSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVE consensus/100% ..sTps...hNhIlaDups+spES.A+SAsVYYSQlhCpsILLlDpuLlosVGDSuElAsKMFDuaVNoFsShaNVsh-KLcpLluTAcstlt+ssshcsVLoTFIsAARt.uhV-SDVE consensus/90% ..NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ.GFVDSDVE consensus/80% ..NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ.GFVDSDVE consensus/70% ..NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ.GFVDSDVE cov pid 2881 . 9 . . . . : . . . . 0 3000 1 ORF1AB_China_Dec2019a 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 2 ORF1a_Finland_29Jan2020 61.9% 99.6% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHSIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 14 ORF1AB_China_11Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 30 ORF1AB_China_08Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 36 ORF1AB_China_02Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 37 ORF1AB_USA_19Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% TNEIVDSVQYAHKHDIQITNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGG- 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% TNEIVDSVQYAHKHDIQITNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGG- 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% TNEIVDSVQYAHKHDIQITNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGG- 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% TNEIVDSVQYAHKHDIQITNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGG- consensus/100% Tp-lV-slphuHppDIplTs-ShNNYh.oYsKs-shospDLGuhIDCsAtplNt.Vh+spshAhIWNstsaMpLS-tL++QIR.As+KsNLsF+LTsuphRtssNllos+hs...lhGG. consensus/90% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGGK consensus/80% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGGK consensus/70% TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGGK cov pid 3001 . . . . : . . . . 1 . . 3120 1 ORF1AB_China_Dec2019a 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 2 ORF1a_Finland_29Jan2020 61.9% 99.6% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 14 ORF1AB_China_11Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 30 ORF1AB_China_08Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 36 ORF1AB_China_02Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 37 ORF1AB_USA_19Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% -APTWFNALRDFTLKGYVLATIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVPTTLAW 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% -APTWFNVLRDFTLKGYVLATIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVPTTLAW 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% -APTWFNVLRDFTLKGYVLATIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVPTTLAW 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% -APTWFNALRDFTLKGYVLATIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVPTTLAW consensus/100% .sssWhp.Lhc........sTllhhhsAslhYLhhPsasMs.hp.apscIlsaKslDsGlhRDlsssDpCFANKHtsFspWapp.hGGsYsNshsCPLhsAVIst.sGhhlPslPsTlhh consensus/90% IVNNWLKQLIK........VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ.RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR consensus/80% IVNNWLKQLIK........VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ.RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR consensus/70% IVNNWLKQLIK........VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ.RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR cov pid 3121 . . : . . . . 2 . . . . 3240 1 ORF1AB_China_Dec2019a 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 2 ORF1a_Finland_29Jan2020 61.9% 99.6% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDIATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 14 ORF1AB_China_11Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 30 ORF1AB_China_08Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 36 ORF1AB_China_02Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 37 ORF1AB_USA_19Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% -VNNQIIFFVSRVFANTGSVCYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQE 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% -VNNQIIFFVSRVFANTGSVCYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQE 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% -VNNQIIFFVSRVFANTGSVCYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQE 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% -VNNQIIFFVSRVFANTGSVCYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQE consensus/100% .sNsphlaFlsRVFussGslCYTP.c.I.YpshusSuClLsuECThF+DApG+.sPYCaDssVL.GuhAYpphRPcsRYsLhDGsh.IpFPpshhEuolRlspThsopYCRaGoCEhupt consensus/90% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA consensus/80% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA consensus/70% TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA cov pid 3241 : . . . . 3 . . . . : . 3360 1 ORF1AB_China_Dec2019a 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 2 ORF1a_Finland_29Jan2020 61.9% 99.6% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 14 ORF1AB_China_11Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYLFLPGVYSVIYLYLTF 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSYVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 30 ORF1AB_China_08Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 36 ORF1AB_China_02Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 37 ORF1AB_USA_19Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% GVCITTNGSWAIFNDHHLNRPGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATF 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% GVCITTNGSWAIFNDHHLNRPGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATF 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% GVCITTNGSWAIFNDHHLNRPGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATF 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% GVCITTNGSWAIFNDHHLNRPGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATF consensus/100% GVCloTsGpWsl.NDaahshPGVaCGsDhlsllpphhssLhQPIshhplosSlVhGhhlshhlThLhYYh.+h+RAFu-Yo.ssshsslhhlhs.hslChsssh.hh.ssYoslYhYhTF consensus/90% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSaVVAFNTLLFLMSFTVLCLTPVYsFLPGVYSVIYLYLTF consensus/80% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF consensus/70% GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF cov pid 3361 . . . 4 . . . . : . . . 3480 1 ORF1AB_China_Dec2019a 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 2 ORF1a_Finland_29Jan2020 61.9% 99.6% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 14 ORF1AB_China_11Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGVMDTTSYREAACC 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 30 ORF1AB_China_08Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 36 ORF1AB_China_02Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 37 ORF1AB_USA_19Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% YFTNEPAFIMHVSWYIMFGPIVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNSL--TNDAYSRFLGLFNKYKYFSGAMETAAYREAAAC 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% YFTNEPAFIMHVSWYIMFGPIVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNSL--TNDAYSRFLGLFNKYKYFSGAMETAAYREAAAC 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% YFTNEPAFIMHVSWYIMFGPIVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNSL--TNDAYSRFLGLFNKYKYFSGAMETAAYREAAAC 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% YFTNEPAFIMHVSWYIMFGPIVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNSL--TNDAYSRFLGLFNKYKYFSGAMETAAYREAAAC consensus/100% YhTN-suFlhHlpWhlMFsPlVPhWhThsYhlshsh+HFaWhhu.a.K++V..hhsGh..soFp-AA.shFllNK-hYhtLRssl..s.stYsRaLuLaNKYKYFSGsM-TsuYREAAsC consensus/90% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV..VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC consensus/80% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV..VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC consensus/70% YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV..VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC cov pid 3481 . 5 . . . . : . . . . 6 3600 1 ORF1AB_China_Dec2019a 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 2 ORF1a_Finland_29Jan2020 61.9% 99.6% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 14 ORF1AB_China_11Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 30 ORF1AB_China_08Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 36 ORF1AB_China_02Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 37 ORF1AB_USA_19Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% HLAKALQTYSETGSDLLYQPPNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTL 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% HLAKALQTYSETGSDLLYQPPNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTL 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% HLAKALQTYSETGSDLLYQPPNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% HLAKALQTYSETGSDLLYQPPNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTL consensus/100% HLAKALpsaSpoGSDlLYQPPpsSITSuVLQSGhhKMuaPSGcVEuCMVQVTCGohTLNGLWLDssVaCPRHVhCsu-ph.sPNY-sLLIphoNHsF.VQt...usspLRVlGHuMQssl consensus/90% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA...GNVQLRVIGHSMQNCV consensus/80% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA...GNVQLRVIGHSMQNCV consensus/70% HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA...GNVQLRVIGHSMQNCV cov pid 3601 . . . . : . . . . 7 . . 3720 1 ORF1AB_China_Dec2019a 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 2 ORF1a_Finland_29Jan2020 61.9% 99.6% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 14 ORF1AB_China_11Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 30 ORF1AB_China_08Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 36 ORF1AB_China_02Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% LKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVA 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% LKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVA 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% LKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVA 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% LKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVA consensus/100% LKLpVDsANPpTPtYpFsplpPGtsFSVLACYNGpPoGsapssMRPNaTIKGSFLsGSCGSVGash-hsslsFCYMHpMELssGsHsGosh-GshYGsFhD+QstQsthTDphhoVNVlA consensus/90% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA consensus/80% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA consensus/70% LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA cov pid 3721 . . : . . . . 8 . . . . 3840 1 ORF1AB_China_Dec2019a 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 2 ORF1a_Finland_29Jan2020 61.9% 99.6% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 14 ORF1AB_China_11Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 30 ORF1AB_China_08Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 36 ORF1AB_China_02Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 37 ORF1AB_USA_19Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% WLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQ--SVDMLAVKTGVAIEQLLYAI-QQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVS 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% WLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQ--SVDMLAVKTGVAIEQLLYAI-QQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVS 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% WLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQ--SVDMLAVKTGVAIEQLLYAI-QQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVS 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% WLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQ--SVDMLAVKTGVAIEQLLYAI-QQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVS consensus/100% WLYAAllNGstWFlp..pTolssFN.hAht.pap.hstsp...ls.LuspTGlAl.phhhul.p.L.sGhpG+pILGSshLEDEFTP.DVshQh.GVshQSuV++shhGTtHWLhhTllo consensus/90% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT consensus/80% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT consensus/70% WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT cov pid 3841 : . . . . 9 . . . . : . 3960 1 ORF1AB_China_Dec2019a 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 2 ORF1a_Finland_29Jan2020 61.9% 99.6% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% SLLVLVQSTQWSLFFFFYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 14 ORF1AB_China_11Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% SLLVLVQSTQWSLFFFFYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFFYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFFYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% SLLVLVQSTQWSLFFFFYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 30 ORF1AB_China_08Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 36 ORF1AB_China_02Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 37 ORF1AB_USA_19Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% TYVIILQATKFTLWNYLFETIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVI-VVKRLYNPSL 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% TYVIILQATKFTLWNYLFETIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVI-VVKRLYNPSL 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% TYVIILQATKFTLWNYLFETIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVI-VVKRLYNPSL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% TYVIILQATKFTLWNYLFETIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVI-VVKRLYNPSL consensus/100% ohllllQuTpaoLa.ahaEsh.h.hh.hlhsh.AFsMhhVKHKHsFLsLFLLPshhslsYhNhVY.Pso.l....htlhsWLs.sss.hpsh+.pDhshYhShsllLll.ss+plYssuh consensus/90% SLLVLVQSTQWSLFFFhYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA consensus/80% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA consensus/70% SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA cov pid 3961 . . . 0 . . . . : . . . 4080 1 ORF1AB_China_Dec2019a 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 2 ORF1a_Finland_29Jan2020 61.9% 99.6% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 14 ORF1AB_China_11Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 30 ORF1AB_China_08Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 36 ORF1AB_China_02Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 37 ORF1AB_USA_19Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% SNFALALCSGVMWLYTYSIGEA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMT 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% SNFALALCSGVMWLYTYSIGEA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMT 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% SNFALALCSGVMWLYTYSIGEA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMT 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% SNFALALCSGVMWLYTYSIGEA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMT consensus/100% pph.hsLhsslhhlYph.hGpA.spsIuhhshlholTSsYohsVhssh.LA+shsahhhtYsP.hhlshsplphIhLlYshLGahCTCYFGlFsLLNhhhRhshGVYDahVSTQEFRaMs consensus/90% RRV.WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN consensus/80% RRV.WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN consensus/70% RRV.WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN cov pid 4081 . 1 . . . . : . . . . 2 4200 1 ORF1AB_China_Dec2019a 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 2 ORF1a_Finland_29Jan2020 61.9% 99.6% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 14 ORF1AB_China_11Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 30 ORF1AB_China_08Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 36 ORF1AB_China_02Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 37 ORF1AB_USA_19Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ANNLTAPRNSWEAMALNFKLIGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQAT 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ANNLTAPRNSWEAMALNFKLIGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQAT 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% ANNLTAPRNSWEAMALNFKLIGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQAT 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% ANNLTAPRNSWEAMALNFKLIGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQAT consensus/100% upsLhsP+NSh-AhtLNhKLlGlGGpPCIKVAshQSKhoDlKCTSVVLLSVLQQL+lEusS+hWA.CVphHNDILhApDsoEAFEKhVSLhusLhohpGsVDlstLsp-hhDs.usLQAh consensus/90% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI consensus/80% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI consensus/70% SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI cov pid 4201 . . . . : . . . . 3 . . 4320 1 ORF1AB_China_Dec2019a 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 14 ORF1AB_China_11Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 30 ORF1AB_China_08Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 36 ORF1AB_China_02Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 37 ORF1AB_USA_19Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% LSEFSHLATFAELEAAQKAYQEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIP 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% LSEFSHLATFAELEAAQKAYQEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIP 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% LSEFSHLATFAELEAAQKAYQEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIP 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% LSEFSHLATFAELEAAQKAYQEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIP consensus/100% hSEFSpLsoaAthtsAQcAYppAhssGDo...VLKtLpKulNlAKsta-+DtAhtRKLE+MADQAMTpMYKQARuEDK+AKlsSAMQTMLFsMl+KLDNDsLNsIIsNARsGClPLslIP consensus/90% ASEFSSLPSYAAFATAQEAYEQAVANGDS.EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP consensus/80% ASEFSSLPSYAAFATAQEAYEQAVANGDS.EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP consensus/70% ASEFSSLPSYAAFATAQEAYEQAVANGDS.EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP cov pid 4321 . . : . . . . 4 . . . . 4440 1 ORF1AB_China_Dec2019a 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 2 ORF1a_Finland_29Jan2020 61.9% 99.6% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 14 ORF1AB_China_11Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFIYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 30 ORF1AB_China_08Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 36 ORF1AB_China_02Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% LCASNKLRVVIPDFTVWNQVVTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNCNT-SSLAYYEPVQGRKMLM 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% LCASNKLRVVIPDFTVWNQVVTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNCNT-SSLAYYEPVQGRKMLM 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% LCASNKLRVVIPDFTVWNQVVTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNCNT-SSLAYYEPVQGRKMLM 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% LCASNKLRVVIPDFTVWNQVVTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNCNT-SSLAYYEPVQGRKMLM consensus/100% LssusKLhVVIPDassappssshsoh.YAuALW-Ip.lsssDscIVp.S-l.hDss.NLsWPLllpshRA.sSAVKLQNNElpPsuL+pMssuAGppQTsCss.suLAYYpsspGt+hlh consensus/90% LTTAAKLMVVIPDYNTYKNTCDGTTFsYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA.NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL consensus/80% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA.NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL consensus/70% LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA.NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL cov pid 4441 : . . . . 5 . . . . : . 4560 1 ORF1AB_China_Dec2019a 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 14 ORF1AB_China_11Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 30 ORF1AB_China_08Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 36 ORF1AB_China_02Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 37 ORF1AB_USA_19Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ALLSDNAYLKWARVEGKDG--FVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKT 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ALLSDNAYLKWARVEGKDG--FVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKT 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% ALLSDNAYLKWARVEGKDG--FVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKT 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% ALLSDNAYLKWARVEGKDG--FVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKT consensus/100% ALLSD.t.LKWARh.tpDG..hl.sELpPPC+FlhssPKGPcl+YLYFlKsLNNLpRG.VLGplAATVRLQAGssTEhsuNSoVLShssFsVDstKAYhDalsuGGtPlTNCVKMLss+T consensus/90% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT consensus/80% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT consensus/70% ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT cov pid 4561 . . . 6 . . . . : . . . 4680 1 ORF1AB_China_Dec2019a 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 2 ORF1a_Finland_29Jan2020 61.9% 99.6% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNGFAV----------------- 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNGFAV----------------- 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% GTGQAITVTPEANMDQESLGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 14 ORF1AB_China_11Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 30 ORF1AB_China_08Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 36 ORF1AB_China_02Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 37 ORF1AB_USA_19Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% GTGIAISVKPESTADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLNESGVLL--------------- 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% GTGIAISVKPESTADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLNESGVLL--------------- 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% GTGIAISVKPESTADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLNRVRGSIVNARIEPCSSGLSTD 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% GTGIAISVKPESTADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLKRVRGSIVNARIEPCSSGLSTD consensus/100% GTG.AIoVpPEushDQEohGGASsCLYCRsHI-HPsspGhCchKGKaVQIPspCspDPVGFsLpNTsCsVCthWhGYGCsCDpLRpshL.pucspsFLpt.ts................. consensus/90% GTGQAITVTPEANMDQESaGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVsG.lssARlpPCuoGhSTD consensus/80% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG.VSAARLTPCGTGTSTD consensus/70% GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG.VSAARLTPCGTGTSTD cov pid 4681 . 7 . . . . : . . . . 8 4800 1 ORF1AB_China_Dec2019a 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 14 ORF1AB_China_11Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 30 ORF1AB_China_08Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 36 ORF1AB_China_02Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 37 ORF1AB_USA_19Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% VVFRAFDICNYKAKVAGIGKYYKTNTCRFVELDDQGHHLDSYFVVKRHTMENYELEKHCYDLLRDCDAVAPHDFFIFDVDKVKTPHIVRQRLTEYTMMDLVYALRHFDQN-SEVLKAILV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% VVFRAFDICNYKAKVAGIGKYYKTNTCRFVELDDQGHHLDSYFVVKRHTMENYELEKHCYDLLRDCDAVAPHDFFIFDVDKVKTPHIVRQRLTEYTMMDLVYALRHFDQN-SEVLKAILV consensus/100% ........................................................................................................................ consensus/90% VVaRAFDIh..psKVAGhuKahKTNsCRF.EhD-psphlDSYFVVKRHThpNYphEcphYsLL+DCsAVA.HDFFhFclDtshsPHIsRQRLTcYTMhDLVYALRHFDps.s-sLKtILV consensus/80% VVYRAFDIY..NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV consensus/70% VVYRAFDIY..NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV cov pid 4801 . . . . : . . . . 9 . . 4920 1 ORF1AB_China_Dec2019a 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 14 ORF1AB_China_11Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 30 ORF1AB_China_08Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 36 ORF1AB_China_02Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 37 ORF1AB_USA_19Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% KYGCCDVTYFENKLWFDFVENPSVIGVYHKLGERVRQAILNTVKFCDHMVKAGLVGVLTLDNQDLNGKWYDFGDFVITQPGSGVAIVDSYYSYLMPVLSMTDCLAAETHRDCDFNKPLIE 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% KYGCCDVTYFENKLWFDFVENPSVIGVYHKLGERVRQAILNTVKFCDHMVKAGLVGVLTLDNQDLNGKWYDFGDFVITQPGSGVAIVDSYYSYLMPVLSMTDCLAAETHRDCDFNKPLIE consensus/100% ........................................................................................................................ consensus/90% pYsCCDssYFppK.WaDFVENPslltVYtpLGERVRQAlLpTVpFCDtMhpAGlVGVLTLDNQDLNGpWYDFGDFl.TpPGSGVslVDSYYShLMPlLohTcsLsAEoHhDsDhsKPhIc consensus/80% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK consensus/70% TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK cov pid 4921 . . : . . . . 0 . . . . 5040 1 ORF1AB_China_Dec2019a 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 14 ORF1AB_China_11Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 30 ORF1AB_China_08Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 36 ORF1AB_China_02Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% WPLTEYDFTDYKVQLFEKYFKYWDQTYHANCVNCTDDRCVLHCANFNVLFAMTMPKTCFGPIVRKIFVDGVPFVVSCGYHYKELGLVMNMDVSLHRHRLSLKELMMYAADPAMHIASSNA 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% WPLTEYDFTDYKVQLFEKYFKYWDQTYHANCVNCTDDRCVLHCANFNVLFAMTMPKTCFGPIVRKIFVDGVPFVVSCGYHYKELGLVMNMDVSLHRHRLSLKELMMYAADPAMHIASSNA consensus/100% ........................................................................................................................ consensus/90% WsLhcYDFT-.+lpLF-+YFKYWDQTYHsNCVNChDDRClLHCANFNVLFuhshP.TsFGPlVRKIFVDGVPFVVSsGYHa+ELGlVhN.DVsLHppRLShKELhhYAADPAMHhASuNh consensus/80% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL consensus/70% WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL cov pid 5041 : . . . . 1 . . . . : . 5160 1 ORF1AB_China_Dec2019a 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 14 ORF1AB_China_11Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 30 ORF1AB_China_08Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 36 ORF1AB_China_02Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% FLDLRTSCFSVAALTTGLTFQTVRPGNFNQDFYDFVVSKGFFKEGSSVTLKHFFFAQDGNAAITDYNYYSYNLPTMCDIKQMLFCMEVVNKYFEIYDGGCLNASEVVVNNLDKSAGHPFN 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% FLDLRTSCFSVAALTTGLTFQTVRPGNFNQDFYDFVVSKGFFKEGSSVTLKHFFFAQDGNAAITDYNYYSYNLPTMCDIKQMLFCMEVVNKYFEIYDGGCLNASEVVVNNLDKSAGHPFN consensus/100% ........................................................................................................................ consensus/90% hLDhRToCFSVAALTsslsFQTV+PGNFNpDFYDFsVSKGFFKEGSSVpLKHFFFAQDGNAAIoDYsYYpYNLPTMCDI+QhLFshEVVsKYF-hYDGGClNAspVlVNNLDKSAGaPFN consensus/80% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN consensus/70% LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN cov pid 5161 . . . 2 . . . . : . . . 5280 1 ORF1AB_China_Dec2019a 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 14 ORF1AB_China_11Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 30 ORF1AB_China_08Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 36 ORF1AB_China_02Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 37 ORF1AB_USA_19Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% KFGKARVYYESMSYQEQDELFAMTKRNVIPTMTQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKMLKSMAATRGATCVIGTTKFYGGWDFMLKTLYKDVDNPHLMGWDYPKCDRAMP 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% KFGKARVYYESMSYQEQDELFAMTKRNVIPTMTQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKMLKSMAATRGATCVIGTTKFYGGWDFMLKTLYKDVDNPHLMGWDYPKCDRAMP consensus/100% ........................................................................................................................ consensus/90% KaGKARlYY-SMSYp-QDtLFAhTKRNVIPThTQMNLKYAISAKNRARTVAGVSIhSTMTNRQaHQKhLKShAATRGATsVIGToKFYGGWc.MLKTlYpDV-NPHLMGWDYPKCDRAMP consensus/80% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP consensus/70% KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP cov pid 5281 . 3 . . . . : . . . . 4 5400 1 ORF1AB_China_Dec2019a 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 14 ORF1AB_China_11Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 30 ORF1AB_China_08Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 36 ORF1AB_China_02Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 37 ORF1AB_USA_19Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% NMCRIFASLILARKHGTCCTTRDRFYRLANECAQVLSEYVLCGGGYYVKPGGTSSGDATTAYANSVFNILQATTANVSALMGANGNKIVDKEVKDMQFDLYVNVYRSTSPDPKFVDKYYA 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% NMCRIFASLILARKHGTCCTTRDRFYRLANECAQVLSEYVLCGGGYYVKPGGTSSGDATTAYANSVFNILQATTANVSALMGANGNKIVDKEVKDMQFDLYVNVYRSTSPDPKFVDKYYA consensus/100% ........................................................................................................................ consensus/90% NMhRIhASLlLARKHsTCCohpcRFYRLANECAQVLSEhVhCGGuhYVKPGGTSSGDATTAYANSVFNIhQAsTANVsALhussGNKIsDK.V+shQacLY.slYRspssDscFVscaYA consensus/80% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA consensus/70% NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA cov pid 5401 . . . . : . . . . 5 . . 5520 1 ORF1AB_China_Dec2019a 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 14 ORF1AB_China_11Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 30 ORF1AB_China_08Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 36 ORF1AB_China_02Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 37 ORF1AB_USA_19Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% FLNKHFSMMILSDDGVVCYNSDYAAKGYIAGIQNFKETLYYQNNVFMSEAKCWVETDLKKGPHEFCSQHTLYIKDGDDGYFLPYPDPSRILSAGCFVDDIVKTDGTLMVERFVSLAIDAY 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% FLNKHFSMMILSDDGVVCYNSDYAAKGYIAGIQNFKETLYYQNNVFMSEAKCWVETDLKKGPHEFCSQHTLYIKDGDDGYFLPYPDPSRILSAGCFVDDIVKTDGTLMVERFVSLAIDAY consensus/100% ........................................................................................................................ consensus/90% aLpKHFSMMILSDDuVVCaNSsYAupGhlAuIpNFKpsLYYQNNVFMSEAKCWsETDLpKGPHEFCSQHThhlKpGDDhhaLPYPDPSRILuAGCFVDDIVKTDGTLMlERFVSLAIDAY consensus/80% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY consensus/70% YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY cov pid 5521 . . : . . . . 6 . . . . 5640 1 ORF1AB_China_Dec2019a 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 14 ORF1AB_China_11Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 30 ORF1AB_China_08Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 36 ORF1AB_China_02Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 37 ORF1AB_USA_19Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% PLTKHEDIEYQNVFWVYLQYIEKLYKDLTGHMLDSYSVMLCGDNSAKFWEEAFYRDLYSSPTTLQAVGSCVVCHSQTSLRCGTCIRRPFLCCKCCYDHVIATPHKMVLSVSPYVCNAPGC 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% PLTKHEDIEYQNVFWVYLQYIEKLYKDLTGHMLDSYSVMLCGDNSAKFWEEAFYRDLYSSPTTLQAVGSCVVCHSQTSLRCGTCIRRPFLCCKCCYDHVIATPHKMVLSVSPYVCNAPGC consensus/100% ........................................................................................................................ consensus/90% PLTKH.s.EYtsVFalYLQYIcKLac-LTGHMLD.YSVMLssDNou+aWE.tFYcshYos.TsLQAVGuCVlCpSQTSLRCGsCIRRPFLCCKCCYDHVIuTsHKhVLSVsPYVCNAPGC consensus/80% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC consensus/70% PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC cov pid 5641 : . . . . 7 . . . . : . 5760 1 ORF1AB_China_Dec2019a 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 14 ORF1AB_China_11Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 30 ORF1AB_China_08Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 36 ORF1AB_China_02Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 37 ORF1AB_USA_19Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% GVSDVTKLYLGGMSYFCVDHRPVCSFPLCANGLVFGLYKNMCTGSPSIVEFNRLATCDWTESGDYTLANTTTEPLKLFAAETLRATEEASKQSYAIATIKEIVGERQLLLVWEAGKSKPP 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% GVSDVTKLYLGGMSYFCVDHRPVCSFPLCANGLVFGLYKNMCTGSPSIVEFNRLATCDWTESGDYTLANTTTEPLKLFAAETLRATEEASKQSYAIATIKEIVGERQLLLVWEAGKSKPP consensus/100% ........................................................................................................................ consensus/90% sVoDVTpLYLGGMSYaChsH+PshSFPLCANG.VFGLYKNhCsGSssls-FNtlATCDWTpuGDYhLANTsTE.LKLFAAETL+ATEEs.K.SYuIATl+Ellu-RpLhLsWEsGKs+PP consensus/80% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP consensus/70% DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP cov pid 5761 . . . 8 . . . . : . . . 5880 1 ORF1AB_China_Dec2019a 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 14 ORF1AB_China_11Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPILNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 30 ORF1AB_China_08Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 36 ORF1AB_China_02Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% LNRNYVFTGYHITKNSKVQLGEYIFERIDYSDAVSYKSSTTYKLTVGDIFVLTSHSVATLTAPTIVNQERYVKITGLYPTITVPEEFASHVANFQKSGYSKYVTVQGPPGTGKSHFAIGL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% LNRNYVFTGYHITKNSKVQLGEYIFERIDYSDAVSYKSSTTYKLTVGDIFVLTSHSVATLTAPTIVNQERYVKITGLYPTITVPEEFASHVANFQKSGYSKYVTVQGPPGTGKSHFAIGL consensus/100% ........................................................................................................................ consensus/90% LNRNYVFTGY+lTKNSKVQlGEYhFE+hDYuDAVsY+uoTTYKLsVGDhFVLTSHoVhsLoAPTlVsQE+YV+ITGLYPhlsls-EFuSpVANaQKsGhpKYsTlQGPPGTGKSHFAIGL consensus/80% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL consensus/70% LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL cov pid 5881 . 9 . . . . : . . . . 0 6000 1 ORF1AB_China_Dec2019a 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHCVYIGDPAQLPAPRTLLTKG 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 14 ORF1AB_China_11Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 30 ORF1AB_China_08Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 36 ORF1AB_China_02Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 37 ORF1AB_USA_19Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% AIYYPTARVVYTACSHAAVDALCEKAFKYLNIAKCSRIIPAKARVECYDRFKVNETNSQYLFSTINALPETSADILVVDEVSMCTNYDLSIINARIKAKHIVYVGDPAQLPAPRTLLTRG 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% AIYYPTARVVYTACSHAAVDALCEKAFKYLNIAKCSRIIPAKARVECYDRFKVNETNSQYLFSTINALPETSADILVVDEVSMCTNYDLSIINARIKAKHIVYVGDPAQLPAPRTLLTRG consensus/100% ........................................................................................................................ consensus/90% AlYYPoARlVYTACSHAAVDALCEKAhKYLsIsKCSRIIPA+ARVECaD+FKVNpT.pQYlFsTlNALPEToADIlVhDElSMsTNYDLSllNARl+AKHhVYlGDPAQLPAPRTLLT+G consensus/80% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG consensus/70% ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG cov pid 6001 . . . . : . . . . 1 . . 6120 1 ORF1AB_China_Dec2019a 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 14 ORF1AB_China_11Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 30 ORF1AB_China_08Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 36 ORF1AB_China_02Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 37 ORF1AB_USA_19Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% TLEPENFNSVTRLMCNLGPDIFLSMCYRCPKEIVSTVSALVYNNKLLAKKELSGQCFKILYKGNVTHDASSAINRPQLTFVKNFITANPAWSKAVFISPYNSQNAVARSMLGLTTQTVDS 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% TLEPENFNSVTRLMCNLGPDIFLSMCYRCPKEIVSTVSALVYNNKLLAKKELSGQCFKILYKGNVTHDASSAINRPQLTFVKNFITANPAWSKAVFISPYNSQNAVARSMLGLTTQTVDS consensus/100% ........................................................................................................................ consensus/90% TLEPE.FNSVsRLMpslGPDhFLuhChRCPtEIVsTVSALVYsNKLhA+K-hSuQCFKhhYKGslTHDsSSAINRPQlshV+pFlTtNPAWpKAVFISPYNSQNAVApphLGLsTQTVDS consensus/80% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS consensus/70% TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS cov pid 6121 . . : . . . . 2 . . . . 6240 1 ORF1AB_China_Dec2019a 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 14 ORF1AB_China_11Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 30 ORF1AB_China_08Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 36 ORF1AB_China_02Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% SQGSEYQYVIFCQTADTAHANNINRFNVAITRAQKGILCVMTSQALFESLEFTELSFTNY---KLQSQIVTGLFKDCSRETSGLSPAYAPTYVSVDDKYKTSDELCVNLNLPANVPYSRV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% SQGSEYQYVIFCQTADTAHANNINRFNVAITRAQKGILCVMTSQALFESLEFTELSFTNY---KLQSQIVTGLFKDCSRETSGLSPAYAPTYVSVDDKYKTSDELCVNLNLPANVPYSRV consensus/100% ........................................................................................................................ consensus/90% SQGSEYpYVIFsQTs-TAHusNlNRFNVAITRAphGILClMospsLa-pLpFTpLphsph...pLQup.VTGLFKDCS+.hoGLpPs.APTalSVDsKaKTps.hss..slPtshsYpRl consensus/80% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL consensus/70% SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL cov pid 6241 : . . . . 3 . . . . : . 6360 1 ORF1AB_China_Dec2019a 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 14 ORF1AB_China_11Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 30 ORF1AB_China_08Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 36 ORF1AB_China_02Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 37 ORF1AB_USA_19Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% ISRMGFKLDATVPGYPKLFITREEAVRQVRSWIGFDVEGAHASRNACGTNVPLQLGFSTGVNFVVQPVGVVDTEWGNMLTGIAARPPPGEQFKHLVPLMHKGAAWPIVRRRIVQMLSDTL 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% ISRMGFKLDATVPGYPKLFITREEAVRQVRSWIGFDVEGAHASRNACGTNVPLQLGFSTGVNFVVQPVGVVDTEWGNMLTGIAARPPPGEQFKHLVPLMHKGAAWPIVRRRIVQMLSDTL consensus/100% ........................................................................................................................ consensus/90% IShMGFKhshpVsGYPphFITREEAlRpVRuWIGFDVEGsHAoRpAsGTNlPLQLGFSTGVNhVs.PsGhVDT..ss.hotluA+PPPG-QFKHLlPLMaKGhsWslVRh+IVQMLSDTL consensus/80% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL consensus/70% ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL cov pid 6361 . . . 4 . . . . : . . . 6480 1 ORF1AB_China_Dec2019a 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 14 ORF1AB_China_11Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 30 ORF1AB_China_08Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 36 ORF1AB_China_02Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 37 ORF1AB_USA_19Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% DKLSDYCTFVCWAHGFELTSASYFCKIGKEQKCCMCNRRAAAYSSPLQSYACWTHSCGYDYVYNPFFVDVQQWGYVGNLATNHDRYCSVHQGAHVASNDAIMTRCLAIHSCFIERVDWDI 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% DKLSDYCTFVCWAHGFELTSASYFCKIGKEQKCCMCNRRAAAYSSPLQSYACWTHSCGYDYVYNPFFVDVQQWGYVGNLATNHDRYCSVHQGAHVASNDAIMTRCLAIHSCFIERVDWDI consensus/100% ........................................................................................................................ consensus/90% cpLSDhssFVhWAHGFELTShpYFsKIG.EppCChCsRRAssaSos.poYACWpHShGaDYVYNPFhlDVQQWGasGNLtoNHDhYCpVHtsAHVASsDAIMTRCLAlHpCFlcRVDWsI consensus/80% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI consensus/70% KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI cov pid 6481 . 5 . . . . : . . . . 6 6600 1 ORF1AB_China_Dec2019a 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 14 ORF1AB_China_11Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTAGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 30 ORF1AB_China_08Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 36 ORF1AB_China_02Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 37 ORF1AB_USA_19Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% EYPYISHEKKLNSCCRIVERNVVRAALLAGSFDKVYDIGNPKGIPIVDDPVVDWHYFDAQPLTRKV---QQLFYT-EDMASRFADGLCLFWNCNVPKYPNNAIVCRFDTRVHSEFNLPGC 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% EYPYISHEKKLNSCCRIVERNVVRAALLAGSFDKVYDIGNPKGIPIVDDPVVDWHYFDAQPLTRKV---QQLFYT-EDMASRFADGLCLFWNCNVPKYPNNAIVCRFDTRVHSEFNLPGC consensus/100% ........................................................................................................................ consensus/90% EYPhIucEhKlNusCRhVp+.VV+AALLAspFshlaDIGNPKuI.hVspssV-W+aaDAQPhocKs...ppLFYo.tshus+FssGlCLFWNCNVs+YPsNuIVCRFDTRVhSphNLPGC consensus/80% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC consensus/70% EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC cov pid 6601 . . . . : . . . . 7 . . 6720 1 ORF1AB_China_Dec2019a 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFIRLQSLENVA 14 ORF1AB_China_11Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 30 ORF1AB_China_08Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 36 ORF1AB_China_02Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 37 ORF1AB_USA_19Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% DGGSLYVNKHAFHTPAYDVSAFRDLKPLPFFYYSTTPCEVHGNGSMIEDIDYVPLKSAVCITTCNLGGAVCRKHATEYREYMEAYNLVSASGFRLWCYKTFDIYNLWSTFTKVQGLENIA 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% DGGSLYVNKHAFHTPAYDVSAFRDLKPLPFFYYSTTPCEVHGNGSMIEDIDYVPLKSAVCITACNLGGAVCRKHATEYREYMEAYNLVSASGFRLWCYKTFDIYNLWSTFTKVQGLENIA consensus/100% ........................................................................................................................ consensus/90% DGGSLYVNKHAFHTPAaDhSAFhsLK.LPFFYYSsoPCEsHGpt.hlpDIDYVPLKSAsCITtCNLGGAVCR+HAsEYR.Yh-AYNhh.uuGFpLWsYKpFDhYNLWsTFh+lQuLENlA consensus/80% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ.VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA consensus/70% DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ.VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA cov pid 6721 . . : . . . . 8 . . . . 6840 1 ORF1AB_China_Dec2019a 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 14 ORF1AB_China_11Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 30 ORF1AB_China_08Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 36 ORF1AB_China_02Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 37 ORF1AB_USA_19Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% FNVVKQGHFIGVEGELPVAVVNDKIFTKSGVNDICMFENKTTLPTNIAFELYAKRAVRSHPDFKLLHNLQADICYKFVLWDYERSNIYGTATIGVCKYTDIDVNSALNI------CFDIR 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% FNVVKQGHFIGVEGELPVAVVNDKIFTKSGVNDICMFENKTTLPTNIAFELYAKRAVRSHPDFKLLHNLQADICYKFVLWDYERSNIYGTATIGVCKYTDIDVNSALNI------CFDIR consensus/100% ........................................................................................................................ consensus/90% FNVVppGHF.G.pGElPVullNsplaTKssssDlphFENKTTLPsNlAFELaAKRsl+shP-hKlLpNLtsDIshphVlWDYcRss.hthuTIGVCphTDIshpss.sI......hFDhR consensus/80% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR consensus/70% FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR cov pid 6841 : . . . . 9 . . . . : . 6960 1 ORF1AB_China_Dec2019a 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYK-EGYAFEHIVYGDFSHS 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 14 ORF1AB_China_11Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 30 ORF1AB_China_08Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 36 ORF1AB_China_02Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 37 ORF1AB_USA_19Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% DNGSLEKFMSTPNAIFISDRKIKKYPCMVGPDYAYFNGAIIRDSDVVKQPVKFYLYKKVNNEFIDPTECIYTQSRSCSDFLPLSDMEKDFLSFDSDVFIKKYGLENYAFEHVVYGDFSHT 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% DNGSLEKFMSTPNAIFISDRKIKKYPCMVGPDYAYFNGAIIRDSDVVKQPVKFYLYKKVNNEFIDPTECIYTQSRSCSDFLPLSDMEKDFLSFDSDVFIKKYGLENYAFEHVVYGDFSHT consensus/100% ........................................................................................................................ consensus/90% ssGpl-hFhss.NulhIo-tplKth.s.VGPc.A.hNGshlhspsVh...spF.hYKKVss.h.p.sEshaTQSRshp-FhPhSpMEhDFLphs.D.FIc+Yt.EsYAFEHlVYGDFSHo consensus/80% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK...TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS consensus/70% VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK...TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS cov pid 6961 . . . 0 . . . . : . . . 7080 1 ORF1AB_China_Dec2019a 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 14 ORF1AB_China_11Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 30 ORF1AB_China_08Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 36 ORF1AB_China_02Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 37 ORF1AB_USA_19Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% TLGGLHLLIGLYKKQQEGHIIMEEMLKGSSTIHNYFITETNTAAFKAVCSVIDLKLDDFVMILKSQDLGVVSKVVKVPIDLTMIEFMLWCKDGQVQTFYPRLQASADWKPGHAMPSLFKV 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% TLGGLHLLIGLYKKQQEGHIIMEEMLKGSSTIHNYFITETNTAAFKAVCSVIDLKLDDFVMILKSQDLGVVSKVVKVPIDLTMIEFMLWCKDGQVQTFYPRLQASADWKPGHAMPSLFKV consensus/100% ........................................................................................................................ consensus/90% pLGGLHLLIGLhK+.pEu.h.hE-hl.hsSTl+NYFIT-spTuu.KsVCSVIDLhLDDFV.IlKSQDLuVVSKVVKVsIDhT.IpFMLWCKDGpVpTFYP+LQuStsWpPGhAMPsLaKh consensus/80% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM consensus/70% QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM cov pid 7081 . 1 . . . . : . . . . 2 7200 1 ORF1AB_China_Dec2019a 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGMLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 14 ORF1AB_China_11Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 30 ORF1AB_China_08Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 36 ORF1AB_China_02Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 37 ORF1AB_USA_19Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% QNVNLERCELANYKQSIPMPRGVHMNIAKYMQLCQYLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTK 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% QNVNLERCELANYKQSIPMPRGVHMNIAKYMQLCQYLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTK consensus/100% ........................................................................................................................ consensus/90% Qph.LE+C-LtNYtpShshP+GlhMNlAKYhQLCQYLNThTLAVPhNMRVIHFGAGSDKGlAPGTuVLRQWLPTshlllDsDLN-FVSDAD.TLhGDCsTV+supphDLlISDMYDPpTK consensus/80% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK consensus/70% QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK cov pid 7201 . . . . : . . . . 3 . . 7320 1 ORF1AB_China_Dec2019a 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ------------------------------------------------------------------------------------------------------------------------ 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ------------------------------------------------------------------------------------------------------------------------ 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 14 ORF1AB_China_11Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQINGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 30 ORF1AB_China_08Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 36 ORF1AB_China_02Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 37 ORF1AB_USA_19Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ------------------------------------------------------------------------------------------------------------------------ 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ------------------------------------------------------------------------------------------------------------------------ 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% NVTGSNESKALFFTYLCNLINNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQLKLKGT 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% NVTGSNESKALFFTYLCNLINNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQLKLKGT consensus/100% ........................................................................................................................ consensus/90% NVTtpN-SKthFFTYlCshIpppLALGGSVAIKITEHSWss-LYcLMG+FAWWTsFsTNsNASSSEuFLlGhNYLGp.+EpIsGhsMHANYIFWRNosPhpLSoYSLFDhSKF.LKL+GT consensus/80% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT consensus/70% NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT cov pid 7321 . . : . ] 7366 1 ORF1AB_China_Dec2019a 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 2 ORF1a_Finland_29Jan2020 61.9% 99.6% ---------------------------------------------- 3 ORF1a_China-Yunnan_17Jan2020 62.1% 99.9% ---------------------------------------------- 4 ORF1AB_Finland_29Jan2020 99.8% 99.8% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 5 ORF1AB_USA-CA_27Jan2020 99.9% 99.9% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 6 ORF1AB_USA-Illinois_21Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 7 ORF1AB_USA-WI_31Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 8 ORF1AB_USA-MA_29Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 9 ORF1AB_China-Hubei-Wuhan_23Dec2019 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 10 ORF1AB_SouthKorea_Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 11 ORF1AB_USA-IL_28Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 12 ORF1AB_Sweden_2020Feb07 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 13 ORF1AB_China-Guangzhou_29Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 14 ORF1AB_China_11Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 15 ORF1AB_USA-CA_23Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 16 ORF1AB_USA-CA_22Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 17 ORF1AB_China-Wuhan_30Dec2019 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 18 ORF1AB_China-Hubei-Wuhan_01Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 19 ORF1AB_Taiwan_05Feb2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 20 ORF1AB_USA-TX_11Feb2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 21 ORF1AB_USA-CA_23Feb2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 22 ORF1AB_China-Guangzhou_27Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 23 ORF1AB_Brazil_28Feb2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 24 ORF1AB_China-Yunnan_17Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 25 ORF1AB_USA-AZ_22Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 26 ORF1AB_Japan_2020Feb10 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 28 ORF1AB_USA-CA_10Feb2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 29 ORF1AB_USA-CA_06Feb2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 30 ORF1AB_China_08Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 31 ORF1AB_Nepal_2020Jan13 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 32 ORF1AB_Taiwan_31Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 33 ORF1AB_China-Hangzhou_20Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 34 ORF1AB_USA-WA_25Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 35 ORF1AB_Australia-Victoria_25Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 36 ORF1AB_China_02Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 37 ORF1AB_USA_19Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 38 ORF1AB_China-Shenzhen_10Jan2020 100.0% 100.0% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN----- 39 ORF1a_MERSctrl_UnitedArabEmirates_2013 58.2% 31.8% ---------------------------------------------- 40 ORF1a_MERSctrl_SaudiArabia_01May2013 58.2% 31.7% ---------------------------------------------- 41 ORF1AB_MERSctrl_SaudiArabia_01May2013 95.9% 44.4% PVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTDVLVNTYRKLR 42 ORF1AB_MERSctrl_UnitedArabEmirates_2013 95.9% 44.4% PVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTDVLVNTYRKLR consensus/100% .............................................. consensus/90% sVhpLKEuQIN-hllSLLSpG+LlIR-NsplslSoDVLVNs..... consensus/80% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN..... consensus/70% AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN..... |
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